X-Ray Crystallography – Nothing says so much about a protein-RNA complex as an elegant crystal structure. We use crystallography to help us visualize the interactions between proteins and RNA of large complexes (e.g. the 30S ribosome sub-domain).
NMR Spectroscopy – While it does not produce pretty crystals, arguably NMR is the best tool to study flexible molecules in solution, and we routinely employ NMR to examine (and even solve!) the structures of our RNA and proteins.
Mass Spectroscopy – More recently, we have delved into mass spectroscopy and developed methods to monitor the different rates of isotope labeling of ribosomal proteins from in vitro reconstitution experiments. Using a novel Fourier-based peak fitting algorithm, we are able to precisely measure the binding rates of all 20 ribosomal proteins of the 30S subunit.